Safe Haskell | None |
---|---|

Language | Haskell2010 |

Run all steps of the HoxCluster algorithms in order.

This will produce the following:

- run the minimal distance algorithm, give the minimal distance score and return all co-optimal paths
- run the end-probability algorithm and return the probability that each node is the begin/end of a chain
- run the edge probability algorithm and give the probability for each
`from :-> to`

edge - with the edge probabilities, run the maximal probability path algorithm, return that probability and all co-optimal paths

TODO -Pretty should yield a structure to be given to the eps or svg generator. This allows more flexibility. Does diagrams offer serialization?

TODO All this should be wrapped and available as a function. not just providing output files.

- runMutationOrder :: Bool -> FillWeight -> FillStyle -> ScaleFunction -> ScaleFunction -> Int -> Int -> Maybe FilePath -> [Char] -> FilePath -> t -> Bool -> [FilePath] -> IO ()
- posScaled :: Double -> Double -> ScaleFunction -> ScaleFunction
- basepairDistanceMFE :: ScaleFunction
- basepairDistanceCentroid :: ScaleFunction
- mfeDelta :: ScaleFunction
- centroidDelta :: ScaleFunction
- squaredPositive :: ScaleFunction -> ScaleFunction
- scaleTemperature :: Double -> ScaleFunction -> ScaleFunction
- scaleByFunction :: (t3 -> t2) -> (t1 -> t -> t3) -> t1 -> t -> t2
- stupidReader :: FilePath -> IO ByteString
- withDumpFile :: Handle -> FilePath -> ByteString -> ByteString -> Landscape -> IO Landscape
- data FillWeight :: *
- data FillStyle :: *
- type ScaleFunction = RNA -> RNA -> Double

# Documentation

runMutationOrder :: Bool -> FillWeight -> FillStyle -> ScaleFunction -> ScaleFunction -> Int -> Int -> Maybe FilePath -> [Char] -> FilePath -> t -> Bool -> [FilePath] -> IO () Source #

posScaled :: Double -> Double -> ScaleFunction -> ScaleFunction Source #

basepairDistanceMFE :: ScaleFunction Source #

Basepair distance

mfeDelta :: ScaleFunction Source #

Scale function for normal mfe delta energies

centroidDelta :: ScaleFunction Source #

Scale function for normal centroid delta energies

squaredPositive :: ScaleFunction -> ScaleFunction Source #

Square positive "contributions", making bad moves more unlikely

scaleTemperature :: Double -> ScaleFunction -> ScaleFunction Source #

Scale by temperature (for probability stuff)

scaleByFunction :: (t3 -> t2) -> (t1 -> t -> t3) -> t1 -> t -> t2 Source #

stupidReader :: FilePath -> IO ByteString Source #

Basepair distance

Stupid fasta reader

:: Handle | |

-> FilePath | The path we store the serialized and compressed dump in |

-> ByteString | ancestral / origin sequence |

-> ByteString | destination sequence |

-> Landscape | the element which is to be serialized in the dump, or which would be the data in the dump |

-> IO Landscape | the data we put in, but maybe taken from the dump file |

`withDumpFile`

is like `idIO :: a -> IO a`

in that it returns the data
we give to the function. However, in case the dump file exists, we read
it and return its contents, instead of recalculating. If it does not
exist, we dump the data in addition to returning it. This forces the
`Landscape`

.

data FillWeight :: * #

Fill weight for our grid. If the fill weight is `logarithmic`

, then
the line length is `1 / (1 + log value)`

otherwise it is `value`

.